Analysis of microarray data - VSN International

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56Analysis of Microarray Data in GenStatOpening the file should result in the following spreadsheet:Within the spreadsheet, the data have two columns foreach slide. To analyse the data it needs to be in astacked format where all the red values are within onecolumn and all the green values are in another. Toreorganise the data, the stack menu can be used. Toopen this dialog select Stack from the Manipulatesection of the Spread menu. The menu right showsthe settings for stacking the columns together. Thereare 16 columns being stacked together. All the greencolumns are first selected and added to the “StackedColumns” list (using the button) and then,likewise, all the red columns are added to the list. Thename Slide has been entered for the factor to indexthe stacked columns. The column ID has beenselected for the Repeat Columns list.Note that the stacked columns can be renamed by double clicking the old namein the “Stacked Columns Names” box and entering the new names in therename dialog (see right).Clicking OK on the stack menu should produce the spreadsheet to the right.The labels of the factor Slide have been created usingthe original column names. However, it may bepreferable to change these labels to remove the ‘G’ todisplay the shorter labels c1...c8, k1...k8. The simplestway to do this is to select Edit Levels and Labels fromthe Factor item on the Spread menu or by clicking onthe toolbar button.
This will open the dialog shown right,where the ‘G’ can be removed from thelabels by editing the appropriate cells.Analysis of Microarray Data in GenStat 57Additional information on the genes and layout of the slides is located within another file,ApoAIGeneNames.tab. The file can be opened using the Open item on the File menu, and should result inthe following spreadsheet:The information from theApoAIGeneNames.tab data set needsto be merged into the stackedspreadsheet. To merge twospreadsheets, click on the spreadsheetthat the data is to be merged into (inthis case the stacked spreadsheet).Select Merge from the Manipulateitem on the Spread menu, whichshould open the dialog on the right.The two spreadsheets are to be mergedusing the column ID to match columnsbetween the spreadsheets.
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Analysis of microarray data - VSN International

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